Saturday, May 06, 2017

Debating philosophers: Epigenetics

Qiaoying Lu and Pierrick Bourrat are philosophers in Australia.1 Their research interests include evolutionary theory and they have taken an interest in the current debate over extending evolutionary theory. That debate has been promoted by a small group of scientists who, by and large, are not experts in evolution. They claim that current evolutionary theory—which they define incorrectly as the 1960s version of the Modern Synthesis—needs to be overthrown or extended by including things like epigenetics, niche construction, developmental biology, and plasticity [New Trends in Evolutionary Biology: The Program].

Lu and Bourrat have focused on epigenetics in their recent paper [Debating philosophers: The Lu and Bourrat paper]. They hope to reach an accommodation by re-defining the evolutionary gene as: "any physical structure that causes a heritable variation." Then they go on to say that, "we define the phenotype of an evolutionary gene as everything that the gene makes a difference to when compared to another gene."

By doing this, they claim that epigenetic changes (e.g. transient methylation) fall with the new definition. Therefore, epigenetics doesn't really represent a challenge to evolutionary theory. They explain it like this ....

With the conceptions of gene, environment and phenotype for gene-centric evolutionary theory in place, we now assess the question of whether evolutionary theory requires a major conceptual change to accommodate epigenetic inheritance. There seems to be a spectrum from conservative to more radical views on this issue. Some think that epigenetic inheritance may have the potential to play an important role in evolutionary processes, but that it is not a contradiction of the classic view on genetic inheritance, only an augmentation (Haig [2007]; Pigliucci [2009]). Others claim that the incorporation of new data and ideas about hereditary variation requires a version of Darwinism that is very different from the gene-centric view (Jablonka and Lamb [2007]; Laland et al. [2014]; Laland et al. [2015]). Our position is twofold. On the one hand, we argue for an extended understanding of the gene in evolutionary theory, rather than a restricted DNA-based account as adopted by most authors. This extension, as we have shown in Section 2.1, corresponds well to the formal evolutionary theory and thus also to the gene-centric tenet of the MS. On the other hand, as we will argue in the following section, given our framework, evolutionary theory can accommodate mechanisms of epigenetic inheritance without a profound conceptual change. Our position is very close to Helanterä and Uller’s ([2010]) suggestion that different inheritance systems may share conceptually similar features but may have different abilities to couple inheritance and selection. Two major challenges to the MS brought up by epigenetic inheritance will be considered.

Here's the problem. I've been following this debate over expending evolutionary theory for almost forty years and I've been paying particular attention to the latest "challenge" that arose in the last decade beginning with the Altenberg 16. I've read the books and I even attended the Royal Society Meeting last November: New trends in evolutionary biology: biological, philosophical and social science perspectives. I've talked to many evolutionary biologists, including some who were at that meeting. I think it's safe to say that most experts in evolutionary biology do not see epigenetics as a threat to current evolutionary theory, with its heavy emphasis on population genetics, and they do not see any need to shift paradigms. Most see epigenetics as a rather minor phenomenon in evolution. Furthermore, it's not new. Modified bases have been known for 40 years and modified histones have been around for almost as long. The definition of "epigenetics" is so nebulous as to be practically useless and hardly different than regulation of gene expression, which was never seen as a threat to evolutionary theory [What the heck is epigenetics?].

But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown.
&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp &nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbspCarl SaganIf I were a philosopher of biology, I would concentrate on the meaning of the current debate and on how proponents of an extended evolutionary synthesis (EES) have framed the discussion around a false view of modern evolutionary theory [More calls to extend the defunct Modern Synthesis]. I would explore the reasons for such a debate and what the EES proponents hope to achieve. I would take care to avoid falling into the trap of believing the hype promoted by the likes of Suzan Mazur and others who seem more interested in seeking publicity than in supporting good science.

Finally, I would be honest with my readers by quoting leading experts in current evolutionary theory to show that most of them dismiss the controversy and ignore the challenges to modern theory. This would require a discussion about real paradigm shifts and how to distinguish between real change and fake change (paradigm shafts). The last thing I would would do is to take sides and try to lecture evolutionary biologists on how to modify their theories to accommodate epigenetics.

This would be a wonderful thesis topic in the history and philosophy of science but it really has much more relevance to epistemology and the behavior of scientists than to actual threats to evolutionary theory. It would make a wonderful case study on where biology has gone wrong and why so many scientists (and philosophers) have fundamental misconceptions about evolution, genetics, and genes. Instead, the Lu and Bourrat paper is just one more example of why biological scientists are skeptical about the contribution philosophers can make to their field.

This is the last of a series of posts on the Lu and Bourrat paper. Here's the complete list.

1. Qiaoying Lu is sometime listed as a member of the Department of Philosophy at Macquarie University in Sidney Australia and sometimes as a graduate student at Sun Yat-Sen University in China. She appears to be a visiting graduate student in Sydney. Pierrick Bourrat is a currently a research fellow at Macquarie University in Sidney although his address on the paper is the University of Sydney. He identifies his research interests as: "Pierrick's main research interest is the philosophy of biology and more particularly the evolutionary side of it. His other areas of interest include the psychology of altruism, cultural evolution and the cognitive science of religion."

11 comments
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From the point of view of population genetics, the argument here seems to mostly be about what one calls the theory. Epigenetic changes have been incorporated into theoretical population genetics by Monty Slatkin in 2009 (paper here and, in quite similar terms, by Tal, Kisdi, and Jablonka (paper here). The results show that epigenetics can bias estimates of heritability, but its effects on a lineage do not last long.

The issue Lu and Borrat raise is whether to rename the Synthesis. Eva Jablonka has campaigned along similar lines.

There is no difference in the implications of the theory, whether you rename it every year, or keep the name the same.

Well its once again the issue also that there is no proven conclusion on how biology works when nobody is watching. As a creationist it teaches that the great conclusion of evolution actually moves in small circles. so small that those who seriously write papers/seek accomplishment in it, with degrees, are not even in the circle.this is why evolutionism is under attack so successfully by tiny numbers of ID scientists, and YEC thinkers a little.This is why its so easy to have seen a error like evolutionism continue since Darwin. Few apply their minds, effectively, to it.

Plasticity is interesting. Its presence, from papers i've seen on nlizards on islands etc, does provide another mechanism for biological change and suggests evolution is not a needed mechanism even within species.In Stephen Gould's research on (snails?)_ where there were hundreds of different types yet still all could breed with each other IT suggests another mechanism is needed.Time shows more dissatisfaction with the old school ideas even within the family.

From the commentary above, I thought LAM has still not differentiated nor characterized the different functions, perspectives, and persuasions of those public intellectual writers, including scientists, scholars especially those in modern biology as referenced above. Briefly let me now focus and discuss several points that LAM has raised; and that I think they require further clarification, as follows:

1) Analysis and characterization of authors’ views on evolutionary biology: Both Qiaoying Lu and Pierrick Bourrat are young aspiring neo-darwinist (theorist, evolutionist, not physiologist nor geneticist or biochemist) philosophers; as such they have taken their best effort and interest in confirming, preserving, and extending the prevailing evolutionary theory (ET) by attempting to incorporate “epigenetics” (a recent discovery of “gene expression/inhibition masking mechanism” that they have had hardly understood, whether empirically or physiologically) into the defunct Modern Synthesis (MS) of ET, initially formulated in 1930s-40s, and further “rhetorically modified” or anthropomorphized in 1960s-70s.

Consequently most subsequent generations of students, scientists, philosophers, and even journalists of biology have had been absorbed, indoctrinated, adapted, and fixated by the prevailing neo-darwinist thinking, theorizing, and anthropomorphizing of the “gene-centric” ET (1976), among whom Richard Dawkins (of “The Selfish Gene” and “hopping meme” fame) has had been -- and still is -- their most outstanding, hard-headed, and “rhetorically-creative” and vocal advocates of their now neo-darwinist gene-centric ET, since after Sir Julian Huxley (1887-1975), the renown British evolutionist, internationalist, eugenicist, and book author of "Evolution: The Modern Synthesis" (1942).

2) “[The current debate over extending ET] has been promoted by a small group of scientists [including philosophers of science] who, by and large, are not experts in evolution.” -- On the contrary they are also a group of scientists, readers, scholars, et al, in developmental biology, genetics, ecology, neuroscience, etc; and naturally their philoscientific views gained from their broad or multidisciplinary reading and inferring on global ET issues, are certainly very much at odds with their concurrent reviewing of the neo-darwinist, theorist perspectives of ET, since 1960s-70s; at which time, when Developmental and Molecular Biology began to revitalize itself in its interdisciplinary research and development programs and enquiries, including -- but not limited to -- the embryological, cellular, physiological, biomedical, genetical, etc pursuits, in and by, the then increasingly more pressing empirical or practical science and philosophy issues!?

3) “The definition of "epigenetics" is so nebulous as to be practically useless and hardly different than regulation of gene expression, which was never seen as a threat to evolutionary theory.” -- I think LAM is mixing oranges with apples here: The mechanism of epigenetics has only been empirically accepted since the turn of the 21st century, especially in the biomedical disciplines; furthermore it is very different from that of the regulation of gene expression in the “central dogma process of genetics”; it is therefore rightly coined “epi (on top of) genetics”.

4) “I would take care to avoid falling into the trap of believing the hype promoted by the likes of Suzan Mazur and others who seem more interested in seeking publicity than in supporting good science.” -- On the contrary I think Mazur is a very vocal public science journalist, who is healthily skeptical and determinedly bent on “dismantling” the defunct neo-darwinist MS of ET, as she certainly anticipates that its time has come: First at the Altenberg 16 conference (2008), but to no avail; and secondly at the Royal Society Meeting last November (2016) on "New trends in evolutionary biology: biological, philosophical and social science perspectives" wherein LAM had also attended, and which had had also proved to be turning out a lot of hot air, while signifying nothing of any paradigm shift(s) at all in the prevailing neo-darwinist thinking that Mazur has had longtime been hoping for in these 2 advanced public science meetings!? Instead she had gotten nothing! -- So don’t give up yet, Suzan Mazur! The best time of paradigm shift has yet to come!

"...while signifying nothing of any paradigm shift(s) at all in the prevailing neo-darwinist thinking that Mazur has had longtime been hoping for in these 2 advanced public science meetings!? Instead she had gotten nothing! -- So don’t give up yet, Suzan Mazur! The best time of paradigm shift has yet to come!"

LOL. Any day now, Suzan. Just keep bullshitting for dollars (or Jesus?).

The EES crowd has lost sight of the bigger picture. For example, why do chimps and humans look different from each other? Is it due to difference in methylation patterns, or is it due to a difference in DNA sequence within their genome? I think most would agree that the differences are due to primary sequence.

So what's the big to-do with epigenetics? Mainly, it's scientists trying to make their work look more important than it is. To be frank, you have to be a bit of a salesperson to get grants or gain respect in any scientific field, but the EES folks have taken it to a whole new level.

Are there epigenetic effects? Sure. Are the significant? No. Most methylation patterns are wiped away during gamete production. Whatever methylation patterns do make it through only last a handful of generations. Which genes are methylated and the effect of methylation still boils down to what the primary sequence is.

IOW, the effects epigenetics on evolution is equivalent to a fart in a hurricane.

Not everyone agrees chimps/humans look different because of these options.the great historical, religious, and well supported in poopulation stats, today is that humans were created separately on the sixth day of creation.chimps a day before, or so,.That also would be why we look different.likeness in biology does not demand like descent.Thats only a option.A creator would also make biology look the same from a common blueprint and that making scientific boundaries. Biology is just like the laws of physics LAWS. Not chance of selectionism.All biology can be seen as alike because of like laws and then KINDS and then drift from that. Another or other mechanisms accounting for the drift from within the existing created blueprint.The issue with evolutionism is still its a line of reasoning from data points. Even if true it would be hard to avoid this. however this line of reasoning is deadly to its claims as a biological investigation that leads to conclusions.

I agree the EES proponents have framed the discussion around a false view of evolutionary theory.I think this points to a problem in the teaching of the theory.I’m assuming the people involved with the EES actually think they are dealing with actual evolutionary theory. And they spend sometime studying the matter.If they get it this wrong (and I have gotten that wrong before) what chance does an average person have of ever getting any idea about what evolutionary theory actually involves?

I hope Koonin’s paper “Splendor and misery…” from an earlier post becomes seminal in the re-evaluation of the teaching of this subject.If we start evolutionary theory with population genetics and we start population genetics with the null hypothesis, then I believe actual evolutionary theory will be better understood by those looking to understand it.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.